Stable Marriage Between 1/2/30/50/100 bp Resolutions

FUNCTION FOR CREATING SEGMENT LABELS VS PROTEINS HEATMAP USING GMTK PARAMETERS OUTPUT

#FUNCTION FOR CREATING LABELS VS PROTEINS HEATMAP
#args csv1, csv2, label_map, must be in quotations (and preferably full paths) when passed in
#label_map can just be the name of the directory for it's particular stable marriage run
make_raw_heatmap <- function(csv1, csv2, label_dir){
  library(ComplexHeatmap)
  gmtkdata1 <- read.csv(csv1, header=TRUE, sep=",", row.names = 1)
  gmtkdata2 <- read.csv(csv2, header=TRUE, sep=",", row.names = 1)
  labelpath <- capture.output(cat("/scratch/mordor/hoffmangroup/wxu/data/2018-06-19_Segway_Analysis/", label_dir, "/overlap-direct/label_map.tab", sep = ""))
  labelmap <- read.csv(labelpath, sep="\t", skip=2, header=FALSE)
  
  # gmtkdata2 <- gmtkdata2[names(gmtkdata1)]
  gmtkdata1 <- gmtkdata1[, order(colnames(gmtkdata1))]
  gmtkdata2 <- gmtkdata2[, order(colnames(gmtkdata2))]
  rownames(gmtkdata1) <- paste("A", rownames(gmtkdata1), sep = "")
  rownames(gmtkdata2) <- paste("B", rownames(gmtkdata2), sep = "")
  ordered.map <- labelmap[order(labelmap$V1), ]
  reorderindex <- (ordered.map$V2 + 1)
  reordered.gmtkdata1 <- gmtkdata1[reorderindex, ]
  gmtkdata1 <- reordered.gmtkdata1
  my_palette <- colorRampPalette(c("mintcream", "lightskyblue", "navyblue"))(n = 299)
  data1 <- data.matrix(gmtkdata1)
  data2 <- data.matrix(gmtkdata2)
  key1 <- capture.output(cat("Run", "1"))
  key2 <- capture.output(cat("Run", "2"))
  ht1 <- Heatmap(data1, name = "Value", cluster_rows = FALSE, cluster_columns = FALSE, show_row_dend = FALSE, show_column_dend = FALSE, column_title = "Trained GMTK Mean Signal A", col = my_palette, row_names_side = "right")
  ht2 <- Heatmap(data2, name = "Value", cluster_rows = FALSE, cluster_columns = FALSE, show_row_dend = FALSE, show_column_dend = FALSE, column_title = "Trained GMTK Mean Signal B", col = my_palette, row_names_side = "left")
  list = ht1 + ht2
  draw(list, gap = unit(1, "cm"), row_title = "Segment Label", row_title_side = "left")
}
# column_title = ""
# column_title_side = "top"
make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-01_Segway_Run_3/gmtk_parameters/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters/gmtk_parameters.stats.csv", "K5seq100bp4100bp23")

Heatmap/row annotation names are duplicated: Value

FUNCTION FOR GENERATING HEATMAP TAKING RATIOS OF THE TWO DATA FRAMES FROM EACH OVERLAP.PY STABLE MARRIAGE RUN

#FUNCTION FOR GENERATING HEATMAP TAKING RATIOS OF THE TWO DATA FRAMES
make_ratio_heatmap <- function(csv1, csv2, label_dir, marriage.name){
  library(ComplexHeatmap)
  gmtkdata1 <- read.csv(csv1, header=TRUE, sep=",", row.names = 1)
  gmtkdata2 <- read.csv(csv2, header=TRUE, sep=",", row.names = 1)
  labelpath <- capture.output(cat("/scratch/mordor/hoffmangroup/wxu/data/2018-06-19_Segway_Analysis/", label_dir, "/overlap-direct/label_map.tab", sep = ""))
  labelmap <- read.csv(labelpath, sep="\t", skip=2, header=FALSE)
  gmtkdata2 <- gmtkdata2[names(gmtkdata1)]
  ordered.map <- labelmap[order(labelmap$V1), ]
  reorderindex <- (ordered.map$V2 + 1)
  reordered.gmtkdata1 <- gmtkdata1[reorderindex, ]
  gmtkdata1 <- reordered.gmtkdata1
  # gmtkdata2 <- gmtkdata2[reorderindex, ]
  my_palette <- colorRampPalette(c("mintcream", "lightskyblue", "navyblue"))(n = 299)
  data1 <- data.matrix(gmtkdata1)
  data2 <- data.matrix(gmtkdata2)
  divide1 <- data1/data2
  # print(divide1)
  divide2 <- data2/data1
  # print(divide2)
  key1 <- capture.output(cat("Run", "1"))
  key2 <- capture.output(cat("Run", "2"))
  ht_list = Heatmap(divide1, name = key1, cluster_rows = FALSE, show_row_dend = FALSE, show_column_dend = FALSE, column_title = "Protein Marks 1 into 2", row_title = "Labels", col = my_palette) +
            Heatmap(divide2, name = key2, cluster_rows = FALSE, show_row_dend = FALSE, show_column_dend = FALSE, column_title = "Protein Marks 2 into 1", row_title = "Labels", col = my_palette)
  draw(ht_list, gap = unit(1, "cm"), column_title = marriage.name, column_title_side = "top")
}
make_ratio_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-01_Segway_Run_3/gmtk_parameters/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters/gmtk_parameters.stats.csv", "K5seq100bp4100bp23", "Stable Marriage Test")

FUNCTION FOR BP OVERLAP, AND NORMALIZED REORDERED LABELS HEATMAP BY ROW AND BY COLUMN

#FUNCTION FOR BP OVERLAP, AND NORMALIZED REORDERED LABELS HEATMAP BY ROW AND BY COLUMN
plot_reorder_labels <- function(csv_and_label_dir){
  library(ComplexHeatmap)
  csv_path <- capture.output(cat("/scratch/mordor/hoffmangroup/wxu/data/2018-06-19_Segway_Analysis/", csv_and_label_dir, "/overlap-direct/overlap.tab", sep = ""))
  labelpath <- capture.output(cat("/scratch/mordor/hoffmangroup/wxu/data/2018-06-19_Segway_Analysis/", csv_and_label_dir, "/overlap-direct/label_map.tab", sep = ""))
  # csv_path <- capture.output(cat("/scratch/mordor/hoffmangroup/wxu/data/2018-06-19_Segway_Analysis/", "K5seq100bp4100bp23", "/overlap-direct/overlap.tab", sep = ""))
  # labelpath <- capture.output(cat("/scratch/mordor/hoffmangroup/wxu/data/2018-06-19_Segway_Analysis/", "K5seq100bp4100bp23", "/overlap-direct/label_map.tab", sep = ""))
  
  labelmap <- read.csv(labelpath, sep="\t", skip=2, header=FALSE)
  overlap <- read.csv(csv_path, sep="\t", skip=1, header=TRUE)
  label <- overlap[,1]
  labelA <- paste("A", label, sep="")
  lastcolindex <- ncol(overlap)
  # none <- overlap[,lastcolindex-1]
  overlap <- as.matrix(overlap[,-c(1, lastcolindex)])
  selection <- overlap[,1:ncol(overlap)-1]
  #row normalization gives you a transpose as a result!
  rnormselection <- t(apply(selection, 1, norm <- function(x){return ((x-min(x))/(max(x)-min(x)))}))
  cnormselection <- apply(selection, 2, norm <- function(x){return ((x-min(x))/(max(x)-min(x)))})
  colnames(selection) <- labelA
  # selection <- cbind(selection, none)
  # print(selection)
  colnames(rnormselection) <- labelA
  # rnormselection <- cbind(rnormselection, none)
  # print(rnormselection)
  colnames(cnormselection) <- labelA
  # cnormselection <- cbind(cnormselection, none)
  ordered.map <- labelmap[order(labelmap$V1), ]
  reorderindex <- (ordered.map$V2 + 1)
  reordered.overlap <- selection[reorderindex, ]
  selection <- reordered.overlap
  rnormselection <- rnormselection[reorderindex, ]
  cnormselection <- cnormselection[reorderindex, ]
  rownames(selection) <- paste("B", ordered.map$V2, sep="")
  rownames(rnormselection) <- paste("B", ordered.map$V2, sep="")
  rownames(cnormselection) <- paste("B", ordered.map$V2, sep="")
  my_palette <- colorRampPalette(c("mintcream", "lightskyblue", "navyblue"))(n = 299)
 htlist = Heatmap(selection, name = "Value", cluster_rows = FALSE, cluster_columns = FALSE, show_row_dend = FALSE, show_column_dend = FALSE, column_title = "BP Overlap of Labels Only", row_title = "Labels Set A vs B", col = my_palette) +
            Heatmap(cnormselection, name =  "Value Norm", cluster_rows = FALSE, cluster_columns = FALSE, show_row_dend = FALSE, show_column_dend = FALSE, column_title = "Column Normalized", row_title = "Labels Set A vs B", col = my_palette) +
            Heatmap(rnormselection, name = "Value Norm", cluster_rows = FALSE, cluster_columns = FALSE,show_row_dend = FALSE, show_column_dend = FALSE, column_title = "Row Normalized", row_title = "Labels Set A vs B", col = my_palette)
  draw(htlist, gap = unit(1, "cm"), column_title = "", column_title_side = "top")
}
plot_reorder_labels("K5seq100bp4100bp23")

BIPARTITE GRAPH WITH THRESHOLD CUT-OFFS FOR ARROWS

#BIPARTITE GRAPH WITH THRESHOLD CUT-OFFS FOR ARROWS
load.data <- function(overlap.dir, threshold.value) {
  overlap <- read.csv(capture.output(cat("/scratch/mordor/hoffmangroup/wxu/data/2018-06-19_Segway_Analysis/", overlap.dir, "/overlap-direct/overlap.tab", sep = "")), sep="\t", skip=1, header=TRUE)
  lastcolindex <- ncol(overlap)
  #grab sum of last column
  total <- sum(as.numeric(overlap$total))
  #get only the columns that are not labels, none, and total
  overlap <- as.matrix(overlap[,-c(1, lastcolindex-1, lastcolindex)])
  #normalize the matrix
  norm_overlap <- apply(overlap, 2, norm <- function(x){return (x/total)})
  #get the row, column indexes respectively
  edge <- as.data.frame(which(norm_overlap>as.numeric(threshold.value), arr.in = TRUE))
  #subtract one from the indices to get the apt label
  edge <- edge -1
  return(edge)
}

get_bipartite <- function(edge){
  require(igraph)                                                                  
  require(gtools)                                                   

  edge[,1] <- paste("B", edge[,1], sep="")
  edge[,2] <- paste("A", edge[,2], sep="")
                                                                                   
  # Order the vertices (which are mixed strings)                                  
  ordered.vertices <- unique(c(mixedsort(edge[,1]), mixedsort(edge[,2])))              
                                                                                   
  # Setup graph                                                                    
  bidata2 <- graph.data.frame(edge, vertices = ordered.vertices, directed = FALSE)
  # print(bidata2)
  V(bidata2)$type <- bipartite_mapping(bidata2)$type                              
  V(bidata2)$label.color <- "black"                                                
  V(bidata2)$color <- ifelse(V(bidata2)$type, "lightblue", "salmon")              
  V(bidata2)$shape <- ifelse(V(bidata2)$type, "circle", "square")                  
  E(bidata2)$color <- "lightgray"                                                  
  V(bidata2)$label.cex <- 1                                                        
  V(bidata2)$frame.color <-  "gray"                                                
  V(bidata2)$size <- 18                                                            
                                                                                   
  # Reorder layout    
  # Add -1 for the 2nd column sort, so that it is in descending instead of ascending order (so 1-> 0); then we get x-axis to y-axis label readings
  l <- layout.bipartite(bidata2)
  # sort the bipartite mapping by the 2nd column first, then the first. Negate all values, then sort in asending so -1 -> -9
  l <- l[order(-l[,2], -l[,1]),]
  # to get a horizontal mapping                                                    
  bd2 <- plot(bidata2, layout = l[, c(2,1)])                                      
  return(bd2)                                                                      
}

# edge <- load.data("K5seq100bp4100bp23", 0.02)
# edge
get_bipartite(load.data("K5seq100bp4100bp23", 0.025))

K562 ChIP-exo 100 bp vs 1 bp Rand Seed 4

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-05-30_Segway_Run_2/gmtk_parameters/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-05-30_Segway_Run_2/gmtk_parameters2/gmtk_parameters.stats.csv", "K5ex100bp1bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("K5ex100bp1bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("K5ex100bp1bp", 0.015))

NULL

K562 ChIP-exo 1 bp vs 2 bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters8/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-28_Segway_Run_7_Res2/gmtk_parameters4/gmtk_parameters.stats.csv", "K5ex1bp2bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("K5ex1bp2bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("K5ex1bp2bp", 0.015))

NULL

#![length distribution](/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/length_distribution8/length_distibution.slide.png)

K562 ChIP-exo 1bp vs 50 bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters8/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-26_Segway_Run_6_Res50/gmtk_parameters4/gmtk_parameters.stats.csv", "K5ex1bp50bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("K5ex1bp50bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("K5ex1bp50bp", 0.025))

NULL

K562 ChIP-exo 100bp vs 1 bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters7/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters8/gmtk_parameters.stats.csv", "K5ex23rand100bp1bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("K5ex23rand100bp1bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("K5ex23rand100bp1bp", 0.022))

NULL

K562 ChIP-exo 2bp vs 100 bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-28_Segway_Run_7_Res2/gmtk_parameters4/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters7/gmtk_parameters.stats.csv", "K5ex2bp100bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("K5ex2bp100bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("K5ex2bp100bp", 0.015))

NULL

K562 ChIP-exo 2bp vs 30 bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-28_Segway_Run_7_Res2/gmtk_parameters4/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-21_Segway_Run_5_Res30/gmtk_parameters4/gmtk_parameters.stats.csv", "K5ex2bp30bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("K5ex2bp30bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("K5ex2bp30bp", 0.02))

NULL

K562 ChIP-exo 2bp vs 50 bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-28_Segway_Run_7_Res2/gmtk_parameters4/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-26_Segway_Run_6_Res50/gmtk_parameters4/gmtk_parameters.stats.csv", "K5ex2bp50bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("K5ex2bp50bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("K5ex2bp50bp", 0.015))

NULL

K562 ChIP-exo 30bp vs 100 bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-21_Segway_Run_5_Res30/gmtk_parameters4/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters7/gmtk_parameters.stats.csv", "K5ex30bp100bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("K5ex30bp100bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("K5ex30bp100bp", 0.02))

NULL

K562 ChIP-exo 30 bp vs 1 bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-21_Segway_Run_5_Res30/gmtk_parameters4/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters8/gmtk_parameters.stats.csv", "K5ex30bp1bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("K5ex30bp1bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("K5ex30bp1bp", 0.025))

NULL

K562 ChIP-exo 30bp vs 50 bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-21_Segway_Run_5_Res30/gmtk_parameters4/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-26_Segway_Run_6_Res50/gmtk_parameters4/gmtk_parameters.stats.csv", "K5ex30bp50bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("K5ex30bp50bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("K5ex30bp50bp", 0.02))

NULL

K562 ChIP-exo 50bp vs 100 bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-26_Segway_Run_6_Res50/gmtk_parameters4/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters7/gmtk_parameters.stats.csv", "K5ex50bp100bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("K5ex50bp100bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("K5ex50bp100bp", 0.02))

NULL

K562 ChIP-seq 100bp vs 1 bp Rand Seed 4

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-01_Segway_Run_3/gmtk_parameters/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-01_Segway_Run_3/gmtk_parameters2/gmtk_parameters.stats.csv", "K5seq100bp1bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("K5seq100bp1bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("K5seq100bp1bp", 0.02))

NULL

K562 ChIP-seq 1bp vs 2bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters2/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-28_Segway_Run_7_Res2/gmtk_parameters/gmtk_parameters.stats.csv", "K5seq1bp2bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("K5seq1bp2bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("K5seq1bp2bp", 0.025))

NULL

K562 ChIP-seq 1bp vs 50 bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters2/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-26_Segway_Run_6_Res50/gmtk_parameters/gmtk_parameters.stats.csv", "K5seq1bp50bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("K5seq1bp50bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("K5seq1bp50bp", 0.035))

NULL

K562 ChIP-seq 100bp vs 1 bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters2/gmtk_parameters.stats.csv", "K5seq23rand100bp1bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("K5seq23rand100bp1bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("K5seq23rand100bp1bp", 0.03))

NULL

K562 ChIP-seq 2bp vs 100 bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-28_Segway_Run_7_Res2/gmtk_parameters/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters/gmtk_parameters.stats.csv", "K5seq2bp100bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("K5seq2bp100bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("K5seq2bp100bp", 0.03))

NULL

K562 ChIP-seq 2bp vs 30 bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-28_Segway_Run_7_Res2/gmtk_parameters/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-21_Segway_Run_5_Res30/gmtk_parameters/gmtk_parameters.stats.csv", "K5seq2bp30bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("K5seq2bp30bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("K5seq2bp30bp", 0.03))

NULL

K562 ChIP-seq 2bp vs 50 bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-28_Segway_Run_7_Res2/gmtk_parameters/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-26_Segway_Run_6_Res50/gmtk_parameters/gmtk_parameters.stats.csv", "K5seq2bp50bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("K5seq2bp50bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("K5seq2bp50bp", 0.03))

NULL

K562 ChIP-seq 30bp vs 100bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-21_Segway_Run_5_Res30/gmtk_parameters/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters/gmtk_parameters.stats.csv", "K5seq30bp100bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("K5seq30bp100bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("K5seq30bp100bp", 0.04))

NULL

K562 ChIP-seq 30bp vs 1bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-21_Segway_Run_5_Res30/gmtk_parameters/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters2/gmtk_parameters.stats.csv", "K5seq30bp1bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("K5seq30bp1bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("K5seq30bp1bp", 0.03))

NULL

K562 ChIP-seq 30 bp cs 50 bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-21_Segway_Run_5_Res30/gmtk_parameters/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-26_Segway_Run_6_Res50/gmtk_parameters/gmtk_parameters.stats.csv", "K5seq30bp50bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("K5seq30bp50bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("K5seq30bp50bp", 0.04))

NULL

K562 ChIP-seq 50bp vs 100 bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-26_Segway_Run_6_Res50/gmtk_parameters/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters/gmtk_parameters.stats.csv", "K5seq50bp1000bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("K5seq50bp1000bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("K5seq50bp1000bp", 0.04))

NULL

MCF7 ChIP-exo 100 bp vs 1bp Rand Seed 4

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-01_Segway_Run_3/gmtk_parameters5/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-01_Segway_Run_3/gmtk_parameters6/gmtk_parameters.stats.csv", "MCex100bp1bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("MCex100bp1bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("MCex100bp1bp", 0.02))

NULL

MCF7 -exo 1bp vs 50 bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters6/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-26_Segway_Run_6_Res50/gmtk_parameters3/gmtk_parameters.stats.csv", "MCex1bp50bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("MCex1bp50bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("MCex1bp50bp", 0.03))

NULL

MCF7 exo 100 bp vs 1 bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters5/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters6/gmtk_parameters.stats.csv", "MCex23rand100bp1bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("MCex23rand100bp1bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("MCex23rand100bp1bp", 0.03))

NULL

MCF7 exo 2bp vs 100 bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-28_Segway_Run_7_Res2/gmtk_parameters3/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters5/gmtk_parameters.stats.csv", "MCex2bp100bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("MCex2bp100bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("MCex2bp100bp", 0.03))

NULL

MCF7 exo 2bp vs 30 bp Rand 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-28_Segway_Run_7_Res2/gmtk_parameters3/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-21_Segway_Run_5_Res30/gmtk_parameters3/gmtk_parameters.stats.csv", "MCex2bp30bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("MCex2bp30bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("MCex2bp30bp", 0.03))

NULL

MCF7 ChIP-exo 2 bp vs 50 bp Rand 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-28_Segway_Run_7_Res2/gmtk_parameters3/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-26_Segway_Run_6_Res50/gmtk_parameters3/gmtk_parameters.stats.csv", "MCex2bp50bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("MCex2bp50bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("MCex2bp50bp", 0.04))

NULL

MCF7 exo 30 bp vs 100 bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-21_Segway_Run_5_Res30/gmtk_parameters3/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters5/gmtk_parameters.stats.csv", "MCex30bp100bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("MCex30bp100bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("MCex30bp100bp", 0.03))

NULL

MCF7 exo 30 bp vs 1 bp Rand 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-21_Segway_Run_5_Res30/gmtk_parameters3/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters6/gmtk_parameters.stats.csv", "MCex30bp1bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("MCex30bp1bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("MCex30bp1bp", 0.025))

NULL

MCF7 exo 30bp vs 50 bp Rand 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-21_Segway_Run_5_Res30/gmtk_parameters3/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-26_Segway_Run_6_Res50/gmtk_parameters3/gmtk_parameters.stats.csv", "MCex30bp50bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("MCex30bp50bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("MCex30bp50bp", 0.04))

NULL

MCF7 exo 50 bp vs 100 bp Rand 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-21_Segway_Run_5_Res30/gmtk_parameters3/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters5/gmtk_parameters.stats.csv", "MCex50bp100bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("MCex50bp100bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("MCex50bp100bp", 0.03))

NULL

MCF7 exo 1bp vs 2bp Rand 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters6/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-28_Segway_Run_7_Res2/gmtk_parameters3/gmtk_parameters.stats.csv", "MCFex1bp2bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("MCFex1bp2bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("MCFex1bp2bp", 0.03))

NULL

MCF7seq 100 bp vs 1 bp Rand Seed 4

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-01_Segway_Run_3/gmtk_parameters3/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-01_Segway_Run_3/gmtk_parameters4/gmtk_parameters.stats.csv", "MCseq100bp1bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("MCseq100bp1bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("MCseq100bp1bp", 0.03))

NULL

MCF7seq 1bp vs 2bp Rand 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters4/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-28_Segway_Run_7_Res2/gmtk_parameters2/gmtk_parameters.stats.csv", "MCseq1bp2bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("MCseq1bp2bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("MCseq1bp2bp", 0.03))

NULL

MCF7 ChIP-seq 1 bp vs 50 bp

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters4/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-26_Segway_Run_6_Res50/gmtk_parameters2/gmtk_parameters.stats.csv", "MCseq1bp50bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("MCseq1bp50bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("MCseq1bp50bp", 0.03))

NULL

MCF7 ChIP-seq 100bp vs 1 bp Rand Seed 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters3/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters4/gmtk_parameters.stats.csv", "MCseq23rand100bp1bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("MCseq23rand100bp1bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("MCseq23rand100bp1bp", 0.03))

NULL

MCF7 ChIP-seq 2bp vs 100 bp

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-28_Segway_Run_7_Res2/gmtk_parameters2/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters3/gmtk_parameters.stats.csv", "MCseq2bp100bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("MCseq2bp100bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("MCseq2bp100bp", 0.03))

NULL

MCF7 ChIP-seq 2 bp vs 30 bp

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-28_Segway_Run_7_Res2/gmtk_parameters2/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-21_Segway_Run_5_Res30/gmtk_parameters2/gmtk_parameters.stats.csv", "MCseq2bp30bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("MCseq2bp30bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("MCseq2bp30bp", 0.04))

NULL

MCF7 ChIP-seq 2 bp vs 50 bp

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-28_Segway_Run_7_Res2/gmtk_parameters2/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-26_Segway_Run_6_Res50/gmtk_parameters2/gmtk_parameters.stats.csv", "MCseq2bp50bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("MCseq2bp50bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("MCseq2bp50bp", 0.05))

NULL

MCF7 ChIP-seq 30 bp vs 100 bp Rand 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-21_Segway_Run_5_Res30/gmtk_parameters2/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters3/gmtk_parameters.stats.csv", "MCseq30bp100bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("MCseq30bp100bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("MCseq30bp100bp", 0.05))

NULL

MCF7 ChIP-seq 30 bp vs 1 bp Rand 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-21_Segway_Run_5_Res30/gmtk_parameters2/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters4/gmtk_parameters.stats.csv", "MCseq30bp1bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("MCseq30bp1bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("MCseq30bp1bp", 0.05))

NULL

MCF7 ChIP-seq 30 bp vs 50 bp Rand 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-21_Segway_Run_5_Res30/gmtk_parameters2/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-26_Segway_Run_6_Res50/gmtk_parameters2/gmtk_parameters.stats.csv", "MCseq30bp50bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("MCseq30bp50bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("MCseq30bp50bp", 0.05))

NULL

MCF7 ChIP-seq 50 bp vs 100 bp Rand 23

make_raw_heatmap("/scratch/mordor/hoffmangroup/wxu/data/2018-06-26_Segway_Run_6_Res50/gmtk_parameters2/gmtk_parameters.stats.csv", "/scratch/mordor/hoffmangroup/wxu/data/2018-06-06_Segway_Run_4/gmtk_parameters3/gmtk_parameters.stats.csv", "MCseq50bp100bp")

Heatmap/row annotation names are duplicated: Value

plot_reorder_labels("MCseq50bp100bp")

Heatmap/row annotation names are duplicated: Value Norm

get_bipartite(load.data("MCseq50bp100bp", 0.04))

NULL

rmarkdown::render(MarriagebtResolutionsFinal.Rmd)